Abstract #5679: Identification of RAN as a neuroblastoma oncogene

AACR Annual Meeting-- Apr 18-22, 2009; Denver, CO Neuroblastoma is a common solid tumor of the sympathetic nervous system that most commonly affects young children and is often lethal. In order to identify candidate oncogenes that may serve as potential therapeutic targets in high-risk neuroblastoma, we are performing a detailed genomic characterization of a large and carefully annotated set of tumors and matched normal tissues (NBL-TARGET: http://ocg.cancer.gov/programs/target.asp). We first assayed DNA copy number in a representative set of 648 primary neuroblastomas using the Illumina HumanHap550 SNP array. Data for each individual tumor was analyzed using the OverUnder algorithm ( Attiyeh, Genome Res., in press ) to identify regions of genomic aberration. In order to identify statistically significant regions of aberration across our sample set in an unbiased manner, we applied the STAC algorithm ( Diskin, Genome Res., 2006 ). Regions determined to be significantly aberrant across multiple samples were then tested for association with clinical and biological co-variates. As expected, regional gain of MYCN ( P < 0.0001), ALK ( P < 0.0001) and 17q21-q25 ( P = 0.0010) were all highly significant. In addition, we identified a novel region of gain at 12q24 ( P < 0.0001). Gain at 12q24 occurred in 15% of neuroblastomas overall and was significantly associated with stage 4 ( P = 0.0047), high-risk ( P = 0.0005), and the MYCN non-amplified subset of high-risk in particular ( P = 0.0021). Paired mRNA expression data on 82 primary tumors demonstrated significant differential expression based on 12q status for twelve of the 107 RefSeq genes tested (11%) which map to 12q24; this regional candidate gene set included RAN, a member of the RAS oncogene family ( P = 0.0040). RAN was also expressed significantly higher in neuroblastoma cell lines with 12q24 gain ( P = 0.0018). We next bisulfate treated a set of 85 primary tumors and analyzed them using the Illumina GoldenGate Methylation Cancer Panel. We observed significantly decreased methylation of RAN in the MYCN non-amplified subset of high-risk when compared to the MYCN amplified high-risk cases ( P = 9.7 x 10-6). Decreased methylation and 12q24 gain showed a trend towards an inverse association in the MYCN non-amplified subset of high-risk ( P = 0.0618), suggesting that multiple mechanisms exist to activate RAN . Finally, to investigate the oncogenic role of RAN in neuroblastoma, we are performing siRNA knockdown of RAN in a set of neuroblastoma cell lines with varying 12q status. There was profound growth inhibition in each of the six cell lines studied to date, all of which have genomic gain and overexpression of RAN . We conclude that RAN functions as an oncogene in high-risk neuroblastoma. We are currently resequencing RAN in primary tumors as well as assessing the potential for RAN -targeted therapy in high-risk neuroblastoma. Supported by U10 CA098543 and R01 CA124709. Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr 5679.